From d4190729a8babc47e4f219af02477160327c0566 Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 08:35:10 -0400
Subject: [PATCH 01/10] Enable Ruff lint checks in CI

---
 .github/workflows/lint.yml               |  6 +++---
 admin/run_ruff_format.sh                 | 15 ++++++++++-----
 benchmarks/cross_similarity_bench.py     |  1 -
 benchmarks/tfd_prepare_mols.py           |  1 -
 nvmolkit/batchedForcefield.py            |  2 --
 nvmolkit/mmffOptimization.py             |  2 --
 nvmolkit/tests/test_mmff_optimization.py |  4 ++++
 nvmolkit/types.py                        |  4 ++++
 nvmolkit/uffOptimization.py              |  1 -
 pyproject.toml                           | 23 +++--------------------
 10 files changed, 24 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 6dfcde41..431935bf 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -143,8 +143,8 @@ jobs:
           set -xeuo pipefail
           bash admin/run_include_check.sh -d
 
-  ruff-format:
-    name: ruff-format
+  ruff:
+    name: ruff
     runs-on: ubuntu-24.04
     timeout-minutes: 30
 
@@ -164,7 +164,7 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install ruff==0.15.8
 
-      - name: Run ruff format check
+      - name: Run Ruff checks
         shell: bash
         run: |
           set -xeuo pipefail
diff --git a/admin/run_ruff_format.sh b/admin/run_ruff_format.sh
index 0255845e..d113619e 100644
--- a/admin/run_ruff_format.sh
+++ b/admin/run_ruff_format.sh
@@ -15,17 +15,19 @@
 # limitations under the License.
 
 
-# Runs ruff format over the codebase.
+# Runs Ruff lint fixes and formatting over the codebase.
 # By default will modify files in-place. Use -d to do a dry-run.
 
 set -ex
 
 EXPECTED_RUFF_VERSION="0.15.8"
-RUFF_ARGS=()
+RUFF_CHECK_ARGS=(--fix)
+RUFF_FORMAT_ARGS=()
 while getopts ":d" opt; do
   case ${opt} in
     d )
-      RUFF_ARGS+=(--check)
+      RUFF_CHECK_ARGS=()
+      RUFF_FORMAT_ARGS+=(--check)
       ;;
     \? )
       echo "Usage: run_ruff_format.sh [-d]"
@@ -39,12 +41,15 @@ ROOT_DIR=$(git rev-parse --show-toplevel)
 if command -v ruff >/dev/null 2>&1; then
   ACTUAL_RUFF_VERSION=$(ruff --version | awk '{print $2}')
   if [ "$ACTUAL_RUFF_VERSION" != "$EXPECTED_RUFF_VERSION" ]; then
-    echo "Warning: expected ruff version $EXPECTED_RUFF_VERSION, found $ACTUAL_RUFF_VERSION. Formatting may not match CI checker." >&2
+    echo "Warning: expected ruff version $EXPECTED_RUFF_VERSION, found $ACTUAL_RUFF_VERSION. Results may not match CI." >&2
   fi
 else
   echo "Error: ruff is not installed; expected version $EXPECTED_RUFF_VERSION." >&2
   exit 1
 fi
 
+echo "Running ruff check:"
+ruff check "${RUFF_CHECK_ARGS[@]}" "$ROOT_DIR"
+
 echo "Running ruff format:"
-ruff format "${RUFF_ARGS[@]}" "$ROOT_DIR"
+ruff format "${RUFF_FORMAT_ARGS[@]}" "$ROOT_DIR"
diff --git a/benchmarks/cross_similarity_bench.py b/benchmarks/cross_similarity_bench.py
index 1e4a2537..c0b744ed 100644
--- a/benchmarks/cross_similarity_bench.py
+++ b/benchmarks/cross_similarity_bench.py
@@ -24,7 +24,6 @@
 from nvmolkit.fingerprints import MorganFingerprintGenerator
 from nvmolkit.similarity import crossCosineSimilarity, crossTanimotoSimilarity
 
-
 SIZES = [2000, 4000, 6000, 8000, 10000, 12000, 14000, 16000, 20000, 24000, 28000, 32000]
 CPU_SINGLE_VALUE_ABOVE = 6000
 
diff --git a/benchmarks/tfd_prepare_mols.py b/benchmarks/tfd_prepare_mols.py
index fc3bbfdd..3ac1996c 100644
--- a/benchmarks/tfd_prepare_mols.py
+++ b/benchmarks/tfd_prepare_mols.py
@@ -37,7 +37,6 @@
 import multiprocessing
 import os
 import pickle
-import sys
 import time
 from functools import partial
 
diff --git a/nvmolkit/batchedForcefield.py b/nvmolkit/batchedForcefield.py
index bc7eaa94..a071d632 100644
--- a/nvmolkit/batchedForcefield.py
+++ b/nvmolkit/batchedForcefield.py
@@ -87,8 +87,6 @@
 from nvmolkit._mmff_bridge import default_rdkit_mmff_properties, make_internal_mmff_properties
 from nvmolkit.types import CoordinateOutput, Device3DResult, FireOptions, HardwareOptions
 
-from nvmolkit import _batchedForcefield  # type: ignore
-
 if TYPE_CHECKING:
     from rdkit.Chem import Mol
     from rdkit.ForceField.rdForceField import MMFFMolProperties as RDKitMMFFMolProperties
diff --git a/nvmolkit/mmffOptimization.py b/nvmolkit/mmffOptimization.py
index 01de9591..c31b6bee 100644
--- a/nvmolkit/mmffOptimization.py
+++ b/nvmolkit/mmffOptimization.py
@@ -33,8 +33,6 @@
     from rdkit.ForceField.rdForceField import MMFFMolProperties
 
 from nvmolkit import _mmffOptimization
-from nvmolkit._mmff_bridge import default_rdkit_mmff_properties, make_internal_mmff_properties
-from nvmolkit.types import CoordinateOutput, Device3DResult, HardwareOptions
 
 
 @overload
diff --git a/nvmolkit/tests/test_mmff_optimization.py b/nvmolkit/tests/test_mmff_optimization.py
index cfbdf758..1136c41c 100644
--- a/nvmolkit/tests/test_mmff_optimization.py
+++ b/nvmolkit/tests/test_mmff_optimization.py
@@ -23,9 +23,13 @@
 from rdkit.ForceField import rdForceField as _rdForceField  # noqa: F401
 from rdkit.Geometry import Point3D
 
+# Preserve this initialization order so converter registration remains
+# explicit in the integration test module.
+# isort: off
 from nvmolkit.embedMolecules import EmbedMolecules
 import nvmolkit.mmffOptimization as nvmolkit_mmff
 from nvmolkit.types import CoordinateOutput, Device3DResult, FireOptions, HardwareOptions
+# isort: on
 
 
 @pytest.fixture
diff --git a/nvmolkit/types.py b/nvmolkit/types.py
index 4e87ce50..9e961685 100644
--- a/nvmolkit/types.py
+++ b/nvmolkit/types.py
@@ -21,9 +21,13 @@
 import numpy as np
 import torch
 
+# Import order is significant: these native modules register converters used by
+# the modules imported after them.
+# isort: off
 from nvmolkit import _arrayHelpers  # noqa: F401
 from nvmolkit import _embedMolecules  # type: ignore
 from nvmolkit import _types
+# isort: on
 
 
 class FireOptions:
diff --git a/nvmolkit/uffOptimization.py b/nvmolkit/uffOptimization.py
index 522efeb8..960cce08 100644
--- a/nvmolkit/uffOptimization.py
+++ b/nvmolkit/uffOptimization.py
@@ -27,7 +27,6 @@
     from rdkit.Chem import Mol
 
 from nvmolkit import _uffOptimization
-from nvmolkit.types import CoordinateOutput, Device3DResult, HardwareOptions
 
 
 @overload
diff --git a/pyproject.toml b/pyproject.toml
index 67e0f5b3..0a499742 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -144,30 +144,13 @@ line-length = 119
 include = ["nvmolkit/**/*.py", "benchmarks/**/*.py", "setup.py"]
 
 [tool.ruff.lint]
-ignore = [
-    "C901",    # Checks for functions with a high McCabe complexity. 
-    "D100",    # Checks for undocumented public module definitions.
-    "E501",    # Checks for lines that exceed the specified maximum character length.
-    "E741",    # Checks for the use of the characters 'l', 'O', or 'I' as variable names.
-    "RUF005",  # Checks for uses of the + operator to concatenate collections.
-]
 select = [
-    "C",   # Pylint conventions
-    "D",   # Documentation formatting
-    "E",   # style stuff, whitespaces
-    "F",   # important pyflakes lints
-    "I",   # import sorting
-    "RUF", # Some Ruff-specific lints, unused noqas, etc.
-    "W",   # Pylint warnings
+    "F", # Pyflakes correctness checks
+    "I", # Import sorting
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["D104"]
-"nvmolkit/tests/test_*.py" = ["D103"]
-"benchmarks/*.py" = ["F841", "D103"]
-
-[tool.ruff.lint.isort]
-lines-after-imports = 1
+"benchmarks/*.py" = ["F841"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"

From 56d6ff645e2e98dfe5514365711139d7482ddd5e Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 08:50:04 -0400
Subject: [PATCH 02/10] Fix Ruff docstring layout findings

---
 nvmolkit/_mmff_bridge.py                  |  2 -
 nvmolkit/batchedForcefield.py             |  6 +--
 nvmolkit/tests/test_batched_forcefield.py | 52 +++++++++++++++--------
 3 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/nvmolkit/_mmff_bridge.py b/nvmolkit/_mmff_bridge.py
index 8b2eaca5..53473ebf 100644
--- a/nvmolkit/_mmff_bridge.py
+++ b/nvmolkit/_mmff_bridge.py
@@ -39,7 +39,6 @@
 
 def default_rdkit_mmff_properties(mol: "Mol"):
     """Create default RDKit MMFF properties for ``mol``."""
-
     properties = rdForceFieldHelpers.MMFFGetMoleculeProperties(mol)
     if properties is None:
         raise ValueError("RDKit could not create MMFF properties for molecule")
@@ -58,7 +57,6 @@ def make_internal_mmff_properties(
     (variant, dielectric, per-term flags); the corresponding getters are not
     wrapped.  We read the settings through the C++ binding layer instead.
     """
-
     return _batchedForcefield.buildMMFFPropertiesFromRDKit(
         properties,
         float(non_bonded_threshold),
diff --git a/nvmolkit/batchedForcefield.py b/nvmolkit/batchedForcefield.py
index a071d632..e8953ed6 100644
--- a/nvmolkit/batchedForcefield.py
+++ b/nvmolkit/batchedForcefield.py
@@ -454,8 +454,7 @@ def _minimize(
 
 
 class MMFFBatchedForcefield(_BatchedForcefieldBase):
-    """Evaluate MMFF energies and gradients, or run BFGS minimization, for a
-    batch of molecules with all their conformers.
+    """Evaluate MMFF energies and gradients or run BFGS minimization for molecule batches.
 
     Properties and constraints are per-molecule and are shared across all
     conformers of that molecule.  Results are nested as
@@ -630,8 +629,7 @@ def minimize(
 
 
 class UFFBatchedForcefield(_BatchedForcefieldBase):
-    """Evaluate UFF energies and gradients, or run BFGS minimization, for a
-    batch of molecules with all their conformers.
+    """Evaluate UFF energies and gradients or run BFGS minimization for molecule batches.
 
     Constraints are per-molecule and are shared across all conformers of
     that molecule.  Results are nested as ``list[list[...]]`` — outer
diff --git a/nvmolkit/tests/test_batched_forcefield.py b/nvmolkit/tests/test_batched_forcefield.py
index fdb5fdda..377e0ac7 100644
--- a/nvmolkit/tests/test_batched_forcefield.py
+++ b/nvmolkit/tests/test_batched_forcefield.py
@@ -165,9 +165,10 @@ def assert_energy_and_gradient_close(got_energy, want_energy, got_grad, want_gra
 
 
 def _assert_batched_compute_matches_rdkit_mmff(mol_specs):
-    """Build a single MMFFBatchedForcefield from ``mol_specs`` and verify that
-    per-mol ``compute_energy``/``compute_gradients`` match RDKit's single-mol FF
-    for each mol, with its configured properties and (optionally) constraint.
+    """Verify batched MMFF energies and gradients against RDKit.
+
+    Build a single MMFFBatchedForcefield from ``mol_specs`` and compare each
+    molecule using its configured properties and optional constraint.
 
     When any mol has a constraint configured, additionally verify that the
     constraint has an observable effect on that mol's energy AND gradient — as
@@ -266,8 +267,11 @@ def _assert_batched_compute_matches_rdkit_mmff(mol_specs):
 
 
 def test_mmff_batched_forcefield_properties_match_rdkit():
-    """Batch of mols with varied per-mol property configurations (default, MMFF variant,
-    dielectric model, term toggles, fragmented+interfrag)."""
+    """Test varied per-molecule property configurations.
+
+    Cover defaults, MMFF variants, dielectric models, term toggles, and
+    fragmented molecules with interfragment interactions.
+    """
     _assert_batched_compute_matches_rdkit_mmff(
         [
             {"factory": load_reference_mol},
@@ -296,9 +300,11 @@ def test_mmff_batched_forcefield_properties_match_rdkit():
 
 
 def test_mmff_batched_forcefield_reads_externally_configured_properties():
-    """Configure RDKit MMFF properties via raw ``rdForceFieldHelpers.MMFFGetMoleculeProperties``
-    plus direct ``SetMMFF*Term``/``SetMMFFDielectricConstant`` calls — no nvmolkit helpers
-    in the path — then hand the object to ``MMFFBatchedForcefield``.
+    """Test externally configured RDKit MMFF properties.
+
+    Configure properties via raw ``rdForceFieldHelpers.MMFFGetMoleculeProperties``
+    plus direct ``SetMMFF*Term``/``SetMMFFDielectricConstant`` calls, with no
+    nvmolkit helpers in the path, then pass the object to ``MMFFBatchedForcefield``.
 
     Needed because of our workaround for RDKit bug https://github.com/rdkit/rdkit/issues/9253
     """
@@ -327,8 +333,11 @@ def test_mmff_batched_forcefield_reads_externally_configured_properties():
 
 
 def test_mmff_batched_forcefield_constraints_match_rdkit():
-    """Batch of mols with all 5 MMFF constraint types applied (one per mol), some also
-    carrying non-default property settings to exercise the properties+constraints path."""
+    """Test all five MMFF constraint types against RDKit.
+
+    Apply one constraint type per molecule, with some molecules also carrying
+    non-default property settings to exercise the properties-plus-constraints path.
+    """
     _assert_batched_compute_matches_rdkit_mmff(
         [
             {
@@ -515,8 +524,11 @@ def _build_constrained_mmff_batch(specs=_MMFF_BATCH_CONSTRAINT_SPECS, hardwareOp
 
 
 def _assert_batched_minimize_matches_rdkit(specs, mols, opt_energies, converged, make_ref_ff):
-    """Compare nvMolKit minimize() result to RDKit minimize per (mol, conformer), with each
-    mol carrying a different constraint from `specs`."""
+    """Compare nvMolKit and RDKit minimization results.
+
+    Compare each molecule and conformer while each molecule carries a different
+    constraint from ``specs``.
+    """
     for mol_idx, (mol, spec) in enumerate(zip(mols, specs)):
         assert len(opt_energies[mol_idx]) == mol.GetNumConformers()
         assert all(converged[mol_idx]), f"Mol {mol_idx} failed to converge"
@@ -531,9 +543,11 @@ def _assert_batched_minimize_matches_rdkit(specs, mols, opt_energies, converged,
 
 
 def test_mmff_batched_minimize_with_constraints_batch_matches_rdkit():
-    """Batch minimize with different constraint types on different-size mols
-    and different conformer counts, comparing each (mol, conformer) energy
-    to RDKit's minimize with the same constraint."""
+    """Test constrained batch minimization against RDKit.
+
+    Use different constraint types, molecule sizes, and conformer counts, then
+    compare each molecule and conformer energy to RDKit with the same constraint.
+    """
     mols, _, ff = _build_constrained_mmff_batch()
     opt_energies, converged = ff.minimize(maxIters=500)
 
@@ -544,9 +558,11 @@ def make_ref(mol, conf_id):
 
 
 def test_mmff_batched_minimize_respects_maxiters_and_forcetol():
-    """maxIters and forceTol must be plumbed through: a single-iteration minimize
-    should not converge and should leave energies closer to the starting point
-    than a generous-iteration minimize."""
+    """Test that maxIters and forceTol are passed through.
+
+    A single-iteration minimization should not converge and should leave energies
+    closer to the starting point than a generous-iteration minimization.
+    """
     perturbed_mols = [
         perturb_conformers(make_embedded_mol("CCCO", num_confs=2)),
         perturb_conformers(make_embedded_mol("c1ccccc1CCO", num_confs=2)),

From 39d911bd1658c0de511e39752c4a8dcdaf8e3c31 Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 08:50:33 -0400
Subject: [PATCH 03/10] Document Ruff-reported Python APIs

---
 nvmolkit/batchedForcefield.py            | 2 ++
 nvmolkit/substructure.py                 | 3 +++
 nvmolkit/tests/test_mmff_optimization.py | 6 +++++-
 3 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/nvmolkit/batchedForcefield.py b/nvmolkit/batchedForcefield.py
index e8953ed6..b0dbb33d 100644
--- a/nvmolkit/batchedForcefield.py
+++ b/nvmolkit/batchedForcefield.py
@@ -512,6 +512,7 @@ def __init__(
         )
 
     def __getitem__(self, idx: int) -> MMFFBatchElement:
+        """Return the force-field element at ``idx``."""
         return super().__getitem__(idx)
 
     def _normalize_properties(
@@ -675,6 +676,7 @@ def __init__(
         self._vdw_thresholds = _normalize_scalar_or_list(vdwThreshold, len(molecules), "vdwThreshold")
 
     def __getitem__(self, idx: int) -> UFFBatchElement:
+        """Return the force-field element at ``idx``."""
         return super().__getitem__(idx)
 
     def _build_native(self):
diff --git a/nvmolkit/substructure.py b/nvmolkit/substructure.py
index 4c59f8e7..31b767bb 100644
--- a/nvmolkit/substructure.py
+++ b/nvmolkit/substructure.py
@@ -79,6 +79,7 @@ def __init__(
         gpuIds: list[int] | None = None,
         algorithm: str = "dfs",
     ) -> None:
+        """Initialize a substructure-search configuration."""
         native = _NativeSubstructSearchConfig()
         native.batchSize = int(batchSize)
         native.workerThreads = int(workerThreads)
@@ -198,9 +199,11 @@ class SubstructMatchResults:
     shape: tuple[int, int]
 
     def __len__(self) -> int:
+        """Return the number of target molecules."""
         return self.shape[0]
 
     def __getitem__(self, target_idx: int) -> _SubstructTargetView:
+        """Return the match view for one target molecule."""
         return _SubstructTargetView(self, target_idx)
 
     def get_pair(self, target_idx: int, query_idx: int) -> list[np.ndarray]:
diff --git a/nvmolkit/tests/test_mmff_optimization.py b/nvmolkit/tests/test_mmff_optimization.py
index 1136c41c..00aa5973 100644
--- a/nvmolkit/tests/test_mmff_optimization.py
+++ b/nvmolkit/tests/test_mmff_optimization.py
@@ -137,7 +137,11 @@ def calculate_rdkit_mmff_energies(
     """Calculate MMFF energies using RDKit for all conformers of all molecules.
 
     Args:
-        molecules: List of RDKit molecules with conformers
+        molecules: List of RDKit molecules with conformers.
+        maxIters: Maximum minimization iterations per conformer.
+        property_settings: Optional MMFF property overrides.
+        nonBondedThreshold: Non-bonded interaction cutoff.
+        ignoreInterfragInteractions: Whether to omit interactions between fragments.
 
     Returns:
         list: List of lists containing energies for each molecule's conformers

From fe1b850503716ffdd6f8e6f18cdb6911c967f61d Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 08:52:12 -0400
Subject: [PATCH 04/10] Remove redundant integer casts

---
 nvmolkit/autotune/_calibration.py | 4 ++--
 nvmolkit/autotune/_core.py        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nvmolkit/autotune/_calibration.py b/nvmolkit/autotune/_calibration.py
index e4a1b5af..5ccaf878 100644
--- a/nvmolkit/autotune/_calibration.py
+++ b/nvmolkit/autotune/_calibration.py
@@ -37,7 +37,7 @@ def auto_subsample(
     """
     if workload_size <= 0:
         raise ValueError("workload_size must be positive")
-    target = min(max_size, max(min_size, int(round(fraction * workload_size))))
+    target = min(max_size, max(min_size, round(fraction * workload_size)))
     target = min(target, workload_size)
     rng = random.Random(seed)
     indices = list(range(workload_size))
@@ -86,6 +86,6 @@ def shrink(indices: Sequence[int], factor: float = 0.5, *, min_size: int = 1) ->
     """
     if factor <= 0.0 or factor >= 1.0:
         raise ValueError("factor must be in (0, 1)")
-    new_size = max(min_size, int(round(len(indices) * factor)))
+    new_size = max(min_size, round(len(indices) * factor))
     new_size = min(new_size, len(indices))
     return list(indices[:new_size])
diff --git a/nvmolkit/autotune/_core.py b/nvmolkit/autotune/_core.py
index fa8a9671..2d24eb35 100644
--- a/nvmolkit/autotune/_core.py
+++ b/nvmolkit/autotune/_core.py
@@ -348,7 +348,7 @@ def collect_int_from_space(spec: Any) -> int:
         high_int = int(high)
         if low_int <= 0 or high_int <= 0:
             raise ValueError(f"Log-uniform range {spec!r} requires strictly positive bounds.")
-        midpoint = int(round(math.sqrt(low_int * high_int)))
+        midpoint = round(math.sqrt(low_int * high_int))
         return max(low_int, min(high_int, midpoint))
     if isinstance(spec, tuple) and len(spec) == 3 and all(isinstance(v, int) for v in spec):
         low, high, step = (int(v) for v in spec)

From e9ed6aa30d5e8064240f2abb4e8cedc870b4fea7 Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 08:52:41 -0400
Subject: [PATCH 05/10] Remove stale Ruff suppressions

---
 nvmolkit/autotune/_core.py      | 2 +-
 nvmolkit/autotune/_ff_common.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nvmolkit/autotune/_core.py b/nvmolkit/autotune/_core.py
index 2d24eb35..d03aab4c 100644
--- a/nvmolkit/autotune/_core.py
+++ b/nvmolkit/autotune/_core.py
@@ -53,7 +53,7 @@ def _require_optuna():
     """Import optuna or raise an :class:`ImportError` with install instructions."""
     if not is_optuna_available():
         raise ImportError(OPTUNA_INSTALL_HINT)
-    import optuna  # noqa: PLC0415
+    import optuna
 
     return optuna
 
diff --git a/nvmolkit/autotune/_ff_common.py b/nvmolkit/autotune/_ff_common.py
index c37845fb..4cfd9db9 100644
--- a/nvmolkit/autotune/_ff_common.py
+++ b/nvmolkit/autotune/_ff_common.py
@@ -100,7 +100,7 @@ def resolve_num_gpus(fixed_gpu_ids: list[int]) -> int:
     if fixed_gpu_ids:
         return max(1, len(fixed_gpu_ids))
     try:
-        import torch  # noqa: PLC0415
+        import torch
 
         return max(1, int(torch.cuda.device_count()))
     except Exception:

From 5ce2813818011940ffcd509a8968667044be1f49 Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 09:16:42 -0400
Subject: [PATCH 06/10] Remove unnecessary Ruff isort guards

---
 nvmolkit/tests/test_mmff_optimization.py |  6 +-----
 nvmolkit/types.py                        | 10 +++++-----
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/nvmolkit/tests/test_mmff_optimization.py b/nvmolkit/tests/test_mmff_optimization.py
index 00aa5973..9853afc8 100644
--- a/nvmolkit/tests/test_mmff_optimization.py
+++ b/nvmolkit/tests/test_mmff_optimization.py
@@ -23,13 +23,9 @@
 from rdkit.ForceField import rdForceField as _rdForceField  # noqa: F401
 from rdkit.Geometry import Point3D
 
-# Preserve this initialization order so converter registration remains
-# explicit in the integration test module.
-# isort: off
-from nvmolkit.embedMolecules import EmbedMolecules
 import nvmolkit.mmffOptimization as nvmolkit_mmff
+from nvmolkit.embedMolecules import EmbedMolecules
 from nvmolkit.types import CoordinateOutput, Device3DResult, FireOptions, HardwareOptions
-# isort: on
 
 
 @pytest.fixture
diff --git a/nvmolkit/types.py b/nvmolkit/types.py
index 9e961685..a1e3f892 100644
--- a/nvmolkit/types.py
+++ b/nvmolkit/types.py
@@ -23,11 +23,11 @@
 
 # Import order is significant: these native modules register converters used by
 # the modules imported after them.
-# isort: off
-from nvmolkit import _arrayHelpers  # noqa: F401
-from nvmolkit import _embedMolecules  # type: ignore
-from nvmolkit import _types
-# isort: on
+from nvmolkit import (
+    _arrayHelpers,  # noqa: F401
+    _embedMolecules,  # type: ignore
+    _types,
+)
 
 
 class FireOptions:

From f4a72cedc03194dae82c426f085202d9b16f1473 Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 09:20:40 -0400
Subject: [PATCH 07/10] Resolve remaining Ruff findings

---
 benchmarks/tfd_profile.py | 2 +-
 nvmolkit/substructure.py  | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/benchmarks/tfd_profile.py b/benchmarks/tfd_profile.py
index 962a9719..e5c14dc2 100644
--- a/benchmarks/tfd_profile.py
+++ b/benchmarks/tfd_profile.py
@@ -174,7 +174,7 @@ def main():
     # === Warmup ===
     if args.warmup > 0:
         with nvtx.annotate("Warmup", color="red"):
-            first_mols = list(configs.values())[0]
+            first_mols = next(iter(configs.values()))
             warmup_mols = first_mols[: min(5, len(first_mols))]
             print(f"\nWarmup ({args.warmup} iteration(s)) with {len(warmup_mols)} molecules...")
             for _ in range(args.warmup):
diff --git a/nvmolkit/substructure.py b/nvmolkit/substructure.py
index 31b767bb..2dea4473 100644
--- a/nvmolkit/substructure.py
+++ b/nvmolkit/substructure.py
@@ -41,10 +41,10 @@
 from nvmolkit._substructure import hasSubstructMatch as _hasSubstructMatch
 
 __all__ = [
-    "SubstructSearchConfig",
     "SubstructMatchResults",
-    "getSubstructMatches",
+    "SubstructSearchConfig",
     "countSubstructMatches",
+    "getSubstructMatches",
     "hasSubstructMatch",
 ]
 

From 58bfd5f67c441313ea11702772368e19df4bc03c Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 09:20:56 -0400
Subject: [PATCH 08/10] Restore full configured Ruff policy

---
 pyproject.toml | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0a499742..3d88d81c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -144,13 +144,27 @@ line-length = 119
 include = ["nvmolkit/**/*.py", "benchmarks/**/*.py", "setup.py"]
 
 [tool.ruff.lint]
+ignore = [
+    "C901",    # Checks for functions with a high McCabe complexity.
+    "D100",    # Checks for undocumented public module definitions.
+    "E501",    # Checks for lines that exceed the specified maximum character length.
+    "E741",    # Checks for the use of the characters 'l', 'O', or 'I' as variable names.
+    "RUF005",  # Checks for uses of the + operator to concatenate collections.
+]
 select = [
-    "F", # Pyflakes correctness checks
-    "I", # Import sorting
+    "C",   # Pylint conventions
+    "D",   # Documentation formatting
+    "E",   # Style and whitespace checks
+    "F",   # Pyflakes correctness checks
+    "I",   # Import sorting
+    "RUF", # Ruff-specific checks
+    "W",   # Pylint warnings
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"benchmarks/*.py" = ["F841"]
+"__init__.py" = ["D104"]
+"nvmolkit/tests/test_*.py" = ["D103"]
+"benchmarks/*.py" = ["F841", "D103"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"

From 068dabba59832882a2181d586d158be82daae80e Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 09:25:16 -0400
Subject: [PATCH 09/10] Enable clean Ruff correctness categories

---
 pyproject.toml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3d88d81c..b2abc3b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -152,13 +152,18 @@ ignore = [
     "RUF005",  # Checks for uses of the + operator to concatenate collections.
 ]
 select = [
-    "C",   # Pylint conventions
+    "A",   # Builtin shadowing
+    "C",   # C-prefixed convention checks
     "D",   # Documentation formatting
+    "DTZ", # Datetime timezone checks
     "E",   # Style and whitespace checks
     "F",   # Pyflakes correctness checks
     "I",   # Import sorting
+    "LOG", # Logging checks
+    "PIE", # Miscellaneous correctness checks
+    "PLE", # Pylint errors
     "RUF", # Ruff-specific checks
-    "W",   # Pylint warnings
+    "W",   # Pycodestyle warnings
 ]
 
 [tool.ruff.lint.per-file-ignores]

From 3add7ba0d7b42232354746d287e71af8138bd43c Mon Sep 17 00:00:00 2001
From: Kevin Boyd <kboyd@nvidia.com>
Date: Fri, 18 Sep 2026 18:24:12 -0400
Subject: [PATCH 10/10] Clarify native converter import ordering

---
 nvmolkit/types.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/nvmolkit/types.py b/nvmolkit/types.py
index a1e3f892..3376da5a 100644
--- a/nvmolkit/types.py
+++ b/nvmolkit/types.py
@@ -21,13 +21,14 @@
 import numpy as np
 import torch
 
-# Import order is significant: these native modules register converters used by
-# the modules imported after them.
-from nvmolkit import (
-    _arrayHelpers,  # noqa: F401
-    _embedMolecules,  # type: ignore
-    _types,
-)
+# These imports populate Boost.Python's global converter registry. Keep this
+# bootstrap sequence developer-controlled so future binding dependencies are
+# not silently reordered by the formatter.
+# isort: off
+from nvmolkit import _arrayHelpers  # noqa: F401
+from nvmolkit import _embedMolecules  # type: ignore
+from nvmolkit import _types
+# isort: on
 
 
 class FireOptions: